Run Breedbase multi-location phenotype variance check — run_breedbase_variance

Reads a Breedbase phenotype file, runs individual ANOVA by environment, performs Hartley Fmax tests, and identifies compatible environment groups for joint analysis.

Usage

run_breedbase_variance_check(
  file,
  trait_col,
  alpha = 0.05,
  location_col = NULL,
  genotype_col = NULL,
  rep_col = NULL,
  block_col = NULL,
  max_group_size = Inf,
  n_sim = 1e+05,
  seed = 123,
  export = FALSE,
  output_dir = NULL
)

Arguments

file: Path to a .xlsx, .xls, or .csv phenotype file, or an already loaded data frame.
trait_col: Trait column to analyze.
alpha: Significance level for Hartley Fmax test.
location_col: Optional location/environment column.
genotype_col: Optional genotype/accession column.
rep_col: Optional replicate column.
block_col: Optional block column.
max_group_size: Maximum environment group size to test.
n_sim: Number of simulations for Hartley critical value.
seed: Random seed for the Hartley critical value simulation. The user's global random number generator state is not modified.
export: Logical. If TRUE, writes CSV files to output_dir.
output_dir: Directory where CSV files should be written. Defaults to NULL, in which case nothing is written; it must be supplied when export = TRUE.

Value

A list containing cleaned data, ANOVA results, Hartley test, all group tests, compatible groups, maximal compatible groups, and detected columns.

Examples

pheno_file <- system.file("extdata", "breedbase_pheno.csv", package = "breedtools")

result <- run_breedbase_variance_check(
  file = pheno_file,
  trait_col = "fresh root yield|CO_334:0000013",
  n_sim = 2000
)

result$env_anova
#> # A tibble: 4 × 12
#>   environment n_genotypes r_eff df_genotype ms_genotype df_error ms_error  mean
#>   <chr>             <int> <dbl>       <int>       <dbl>    <int>    <dbl> <dbl>
#> 1 Geneva               12     2          11        20.6       11     1.14  31.5
#> 2 Ibadan               12     2          11        39.7       11     6.45  22.1
#> 3 Ithaca               12     2          11        14.3       11     1.25  27.7
#> 4 Ubiaja               12     2          11        54.3       11     4.78  24.3
#> # ℹ 4 more variables: cv_percent <dbl>, sigma2_g <dbl>, f_value <dbl>,
#> #   p_value <dbl>
result$maximal_compatible_groups
#> # A tibble: 2 × 9
#>   group_id     k environment_list        min_ms_error max_ms_error fmax_observed
#>   <chr>    <int> <chr>                          <dbl>        <dbl>         <dbl>
#> 1 G9           3 Geneva | Ithaca | Ubia…         1.14         4.78          4.20
#> 2 G5           2 Ibadan | Ubiaja                 4.78         6.45          1.35
#> # ℹ 3 more variables: fmax_critical <dbl>, alpha <dbl>, homogeneous <lgl>

# Export CSV files to a temporary directory
out_dir <- file.path(tempdir(), "variance_check")
result <- run_breedbase_variance_check(
  file = pheno_file,
  trait_col = "fresh root yield|CO_334:0000013",
  n_sim = 2000,
  export = TRUE,
  output_dir = out_dir
)
list.files(out_dir)
#> [1] "hartley_all_group_tests_fresh root yield|CO_334:0000013.csv"          
#> [2] "hartley_maximal_compatible_groups_fresh root yield|CO_334:0000013.csv"
#> [3] "individual_anova_fresh root yield|CO_334:0000013.csv"                 
unlink(out_dir, recursive = TRUE)